The study of the interactions among metals, minerals, and humic substances is essential in understanding the migration of inorganic pollutants in the geosphere. A considerable amount of organic matter in the environment is associated with clay minerals. To understand the role of organic matter in the environment and its association with clay minerals, a hybrid clay-based material (HCM), montmorillonite (STx-1)–melanoidin, was prepared from l-tyrosine and l-glutamic acid by the Maillard reaction. The HCM was characterized by elemental analysis, nuclear magnetic resonance, x-ray photoelectron spectroscopy (XPS), scanning transmission x-ray microscopy (STXM), and thermal analysis. The presence of organic materials on the surface was confirmed by XPS and STXM. The STXM results showed the presence of organic spots on the surface of the STx-1 and the characterization of the functional groups present in those spots. Thermal analysis confirmed the existence of organic materials in the montmorillonite interlayer, indicating the formation of a composite of melanoidin and montmorillonite. The melanoidin appeared to be located partially between the layers of montmorillonite and partially at the surface, forming a structure that resembles the way a cork sits on the top of a champagne bottle.